I am trying to work thru some issues with our battery system. We have 2 house batteries and one battery that I assume only is used for generator starting. After not using the generator all summer, I went to start it the other day and it would not turn over.

I went down today and with the battery switch in off, I get 13.9v on each house battery and 11.8 on generator starting battery. So I assume the charger is charging both house batteries, but NOT generator starting battery.

Looking for suggestions on how to troubleshoot, Generator battery has a positive wire coming off of it and two ground wires connected to it. I took off the terminals and cleaned them well.

I guess the question is how does battery charger get routed to each battery for charging.

Check if the charger has two outputs, then you could route one to the generator battery. If the charger has only one output going to the house bank, you can put an automatic charging relay between the house bank and the generator battery. It will allow the generator battery to be charged when the engine is running or the charger is on. It will disconnect otherwise to prevent the generator battery from being discharged by house loads.